Wednesday, April 9, 2014

The phylogenetics of angiosperm classification schemes

Alain Cuerrier, Luc Brouillet and Denis Barabe (1998. Numerical and comparative analyses of the modern systems of classification of the flowering plants. Botanical Review 64: 323-355) have provided a genealogy of the various classifications that have been produced for the angiosperms (flowering plants). This is a theoretical construction, intended to express the lines of intellectual influence, either directly expressed by the authors of the classifications, or inferred by comparison of the classifications themselves.

As shown here, it is a classic directed acyclic graph, most of which is tree-like, although some parts are distinctly bushy. Of interest to us, there are also places where hybridizations are indicated.

Cuerrier et al. analyzed the structure of the four modern classifications (by Cronsquist, Dahlgren, Takhtajan, and Thorne) in comparison to their immediate predecessors (by Bessey, Engler, Hallier, and also Gobi). This was a study of affinity relationships, rather than genealogy, and one of their study questions was whether the affinity relationships matched the genealogical ones.

In this regard it is interesting to note that they used clustering and ordination techniques to analyze their quantitative data (comparing the classifications), but they did not use any network techniques. Yet, this would seem to be an obvious strategy, given that they were expecting reticulating relationships.

Unfortunately, none of the datasets shown in the paper is complete, and so I cannot provide a network analysis for them.

The authors summarized their suite of multivariate analyses as an interaction network, as shown next. For each pair of classifications, four statistical tests were performed, and the thickness of the arrows in the network indicates the degree of significant similarity detected: dotted arrow = 2/4 tests show similarity, thin arrow = 3/4 tests, and thick arrow = 4/4 tests.

These semi-quantitative relationships can also be expressed as an unrooted phylogenetic network. I simply took the pairwise similarity scores (0.0, 0.25, 0.5, 0.75, 1.0) and analyzed them using a NeighborNet network. The four modern classifications are highlighted in red.

This more clearly illustrates the various points made by Cuerrier et al. In particular, they note that the intellectual genealogy is not reflected in the affinity relationships of the modern classifications. For example, the Cronquist and Takhtajan classifications are much more similar to that of Hallier than to that of Bessey, whereas Cronquist explicitly cites Bessey as a major influence on his work. Instead, Cronquist's classification is more similar to that of Engler, who does not appear to be genealogically related at all. The distinction between the Thorne and Dahlgren classifications and those of Takhtajan and Cronquist is also obvious.